We describe a simple and practical method for the analysis of phosphorus-containing amino acid-type herbicides and their decomposition products without derivatization by capillary electrophoresis/mass spectrometry using a chemically modified capillary having amino groups. The compounds were glyphosate (GLYP), glufosinate (GLUF), bialaphos (BIAL), aminomethylphosphonic acid (AMPA) and 3-methylphosphinicopropionic acid (MPPA). AMPA and MPPA are the decomposition products of GLYP and GLUF, respectively. The optimum running conditions were found to be 100 mM formic acid adjusted to pH 3.4 with 100 mM ammonia with an applied voltage of -30 kV using an amino capillary (FunCap-CE/Type A) and mass spectrometry. The five compounds were separately determined within 10 min. Relative standard deviations of the migration times of analytes were less than 0.52%. Total analysis time of the proposed method was 1/6 to 1/3 of that of gas chromatography/mass spectrometry methods. The method was applicable for the analysis of these compounds in soil and tea beverage samples. The decomposition rates of GLYP, GLUF and BIAL in soil are discussed.